A fairy named Navi is trying to wake up a sleeping princess, known as "Protagonist" in the game. Navi urges Protagonist to wake up because she is dying of boredom. When Protagonist finally does wake up, Navi reveals she has already created a small world for Protagonist to explore. Navi teleports herself and Protagonist into this world where she tells Protagonist to hurry and get to school, since Navi has made so that Protagonist is a student in this world. Navi also mentions that only Protagonist can see her; no one else can see or hear Navi. The two head off towards school.
Navi explains that Protagonist's purpose in this world is to create bonds with the characters within the world, since Protagonist needs to practice her social skills after her long slumber. Once Protagonist has gathered enough friends, she will set out to defeat evil, because Navi needed to have an end goal for her game. Protagonist then finds a
named Jonathan attacking , who is after the toast in QP's mouth. Navi tells Protagonist to save QP so that she might become her ally. Protagonist is unable to fight directly because of the world's rules and must use allies to fight for her; Allies appear in the form of cards in this world once a bond has been forged. Unfortunately, Protagonist does not have any allies so Navi suggests creating a bond right now with QP; adding that it should be easy since QP looks dumb enough. Protagonists merely hugs QP and to the disbelief of even Navi, a bond is instantly forged with QP. Jonathan is subsequently defeated and QP and the Protagonist both head off to school together after realizing they both attend the same school.
They reach the school and QP asks which class Protagonist is in. To further simplify things for Protagonist, Navi messes with the world's setting so Protagonist is conveniently in the same class as QP, and a transfer student at that. Inside the classroom, Shifu, who is the teacher, asks Protagonist to introduce herself to the class. Protagonist in turn says nothing due to her lack of social skills. Shifu moves on to explain that the day's curriculum will be battle training. Everyone in the school is now considered an enemy, and the first to get four wins is to report to the gym and receive a reward. Navi, having zero confidence in Protagonist's social skills or her chances with just QP on her side, decides to make an arbitrary system called the Mixdus, where Protagonist can just buy allies with stars.
On the first floor, they find
, who QP is mad at for eating more pudding than her on a certain night. Syura in turn is similarly mad at QP for entirely failing to QA a game they made together. Both lamenting the circumstances which have forced them at odds, QP battles Syura, and Syura faints after being defeated. On the second floor, they find and arguing over whether or not Fernet is a proper lady of nobility. Krilalaris says that QP is more noble than Fernet, and this angers Fernet. Fernet fights QP to prove her nobility, and Krilalaris also fights QP because of the temptation of QP's red bean bread that QP had bought. After the battle, Fernet figures out that Krilalaris just wanted red bean paste all along and offers to treat her any time if it allows her to be treated as a noble by Krilalaris. On the third floor, they find , the student president, and vice president . Kyoko does not appreciate Kyousuke treating her with such familiarity at school and is ashamed to call Kyousuke her twin brother. Kyousuke mistakes QP for , and becomes overly excited that Kyupita has returned to him. QP remarks that that Kyoko looks just like Kyousuke, and Kyoko takes offense. QP battles both of the siblings, with Kyousuke wanting to take Kyupita(?) by force and Kyoko attacking QP out of indignation over the comparison. After the siblings' defeat, Kyousuke demands to know why Kyupita won't return to him. Kyoko tries to calm Kyousuke down by insisting that QP is a girl. Kyousuke gropes QP to confirm that QP is in fact a girl, and then calms down. On the school rooftop, they find and . Mei has been calling everyone who comes to the rooftop her nemesis and battled them. Mira hasn't been able to get into any fights because people are afraid of battling them as the head of the rhythmic gymnastics fighting club, so they hope to team up with Mei, a naturally antagonistic individual. After Mei and Mira's defeat, Mira invites QP to their club after seeing how strong QP is, but QP rejects the offer, in fear of her tail being chopped off by Mira's boomerangs. Mei asks to join Mira's club after QP's rejection, but Mira rejects Mei. QP and Protagonist have their four wins, so they head to the gym. They were the first ones to come to the gym so their reward is a personal battle with Shifu and . After defeating Shifu, Reika appears, introducing herself to QP and Protagonist. Navi congratulates Protagonist for completing the school phase of the world and starts preparing for the next phase.
On the school rooftop, QP and Protagonist see an airplane falling from the sky. The plane barely managing to land next to them, the pilot is revealed to be
. Marc introduces herself to QP and Protagonist and apologizes for surprising them. Marc needs to check on her plane, Red Barrel, as the controls failed after colliding with something in the sky. Navi suggests to Protagonist to fix Red Barrel to gain Marc as an ally, and Protagonist immediately does so with just one touch of her hand. Red Barrel's controls work again and Marc becomes an ally. QP and Protagonist notice the school is gone and that they are now in the middle of a forest. Marc leads the group to the closest town, after seeing that QP and Protagonist were lost. QP and Marc guess that their worlds are parallel worlds since QP and her friends could fly and Marc cannot without the use of vehicles. QP is interested in figuring out how to get back home, and the group make plans to head towards town, since it's better than doing nothing. They find Grain, who has been looking for Marc, but suddenly , , and Mescal are seen trying to run away. Grain explains that they broke into the Guild and stole something, and he wants Marc to help capture them. The thieves then send a flock of seagulls to stall the Protagonist's group. Navi explains to Protagonist that the goal of this section is to capture the thieves and suggests to search around town. At the Guild, they find who challenges Marc saying how his new partner, , will make the Blue Crow undefeatable. Marc confuses Iru for a boy, Iru corrects Marc, and Marc apologizes. Peat awkwardly admits he also didn't know Iru was a girl and Iru asks if she can leave. Peat promises to Iru that he will show her the Guild's secret mechanic if she stays and helps him win, so Iru agrees to stay and fight. After the fight, Marc and QP praise Iru for her aim and Iru appreciates the compliments, complementing back that she likes Marc's plane. Marc then remembers that they were chasing thieves, so they leave, completely ignoring Peat. On the main street, QP and notice each other, and both agree to fight to the death since they both look so similar. After their fight, they both give each other handshakes, both saying that it was the best fight they'd ever had. Unable to find any clues to the thieves' whereabouts, the group relaxes on a street corner, feeling the calm breeze. An odd sense of serenity is established as it is revealed that the thieves are also relaxing here, then Marc breaks this calm by noticing the thieves. Being unable to run away, Tomato and Mimyuu both attack the group but lose, and Mescal is brought to tears. Then Captain and show up, with Tequila demanding to know who made Mescal cry and Yuki demanding to know who harassed her subordinates. Both Tequila and Yuki attack the group and lose. It was revealed that the Sky Pirates and Waruda had both teamed up to kidnap Reika because she has a special power. Tequila asks the group to let him go because he does not want the Guild to have Reika, but suddenly the sky turns dark and gloomy.
Protagonist's group hears and explosion and notices someone falling from the sky. Protagonist catches the falling person, who is revealed to be
. Sora thanks Protagonist for saving her and becomes Protagonist's ally. The group hears another explosion and Sora urges the group to follow her to someplace safe but then Marc and QP notices that Yuki, Tequila, and Reika are not where to be found. Sora takes the group to Yukito's facility, where he introduces himself to Protagonist's group. QP and Marc explains to Sora and Yukito the events that led them here and Yukito understands their situation. Yukito explains the crossing between worlds is thanks to something called the , citing that lately, people have been mysteriously disappearing and appearing. Marc remembers that her plane original fell because she collided with a and Sora remembers that she fell because she was shot by a rocket that was 16 times larger than normal. Yukito suspects that Marc and Sora were probably both caught in the Mix Phenomenon. Sora is worried that something terrible will happen if the Mix Phenomenon progresses. Yukito explains that he has been researching the Mix Phenomenon and he thinks he found something that might lead to a solution to this event, a person who is able to cross the worlds at will. This person has been cooperating with Yukito but then suddenly Yukito has been notified that this person has been kidnapped. Yukito orders to seal all the exits and to check all the cameras. The exits are then sealed but the cameras have suddenly been turned off. He asks the Protagonist's group to search the facility as Yukito repairs the cameras. In the facility's docks, the group finds Merchant and , these two have been trading with the base and asks the group to open the sealed entrances so they can go to their next customer. Sora explains that, because of an emergency, the entrances cannot be opened. Merchant and Arthur did not like Sora's response, stating that time is money, and they have no choice but to blow up the sealed entrance. The group defeats the two salesmen and assures them that this emergency will be resolved as fast as possible. In the operating room, the group finds and , where Alte is trying to find an exit to go back to her husband. The reason why they are here is because Alte was attempting to cook for her husband, but got in an accident and burned her face, as well as half of Sham's body, since she was nearby. Alte desperately wants to go to her husband and resolves to just go by force, with Sham helping her because the power of love is just too great for Sham to resist. The group defeats the two and asks them to wait just a bit longer. In the canteen, Marc spots someone she thinks she recognizes, but the person runs away after telling Bourbon, , and to get rid of Protagonist's group. The group defeats the three and ran after the direction of the kidnapper. Yukito calls Sora, telling her that the cameras are fixed and he suspects the kidnapper is on the roof. Up on the roof, the culprit is revealed to be Grain. Marc asks why would Grain resort to kidnapping but Grain explains that this was for the sake of the Guild. The kidnapped person is revealed to be Reika, she is the key to the Mix Phenomenon. Grain explains that once Reika's ability is activated, all the worlds would chaotically fuse together just like mixed juice. She is the cause for the Mix Phenomenon and Grain wants to take control of her for the Guild. Yuki and Bourbon shows up, stating that the Guild would not control the world with Reika, they would be the ones to do so instead. Tequila and Yuki prepares to fight Grain but then Reika awakens. Reika's ability has been activated and she changes into and blows Yuki and Tequila away. Grain resolves to kill Star Breaker before she gets out of control but Star Breaker effortlessly stops him. Star Breaker is thrilled to fight QP, Marc, and Sora, but the numbers are unfair to her and asks Grain to join her side, which he agrees to. The group defeats Star Breaker and Grain, where Star Breaker reverts into Reika. Suddenly, appears and cuts Reika, separating her ability and personality in an attempt to stop the Mix Phenomenon from progressing. However, her plan backfires, Star Breaker and Reika are now two separate entities, with Star Breaker having the abilities to manipulate the Mix phenomenon. After an explosion, the group sees the world shattered and ruined, then they suddenly found themselves back in Marc's world. Sweet Breaker appears again and she introduces herself as the god of happiness and luscious history. Sweet Breaker explains that she is here to stop the Mix Phenomenon and the vision the group saw after the explosion is of whats to come if the Mix Phenomenon continues. She can only interfere with reality for a short amount of time before recharging her abilities, so it will be a while before she can do something again, which is why she came to the Protagonist's group to ask for assistance. Sweet Breaker asks the group to defeat Star Breaker, to which the whole group agrees to. Star Breaker is somewhere inside the town, and the group begins searching for her.
In a back alley, Sora attempts to imitate QP but QP asks Sora to stop, saying that she will not be able to tell the difference.
and shows up with Tsih pointing out that QP and Sora are bland and herself and Kae are not bland at all and Kae laughing in agreement with Tsih. Marc calls Kae and Tsih wacky, which Kae laughs at and Tsih finds insulting. After their battle, QP and Sora ends up sad after concluding that the fight was meaningless and they were bland and similar after all. The group arrives at the Guild again and QP says that Mikky Mousse would live in a place like this, and this excites Sora. Sora really wants to pet Mikky Mousse and then suddenly appeared. The group thinks Poppo is Mikky but then she steals Marc's rocket. shows up and asks if Poppo found anything again. Kai then introduces himself as main character from another world, being in this world as an extra. Marc tells the group to just forget about Kai and to help her get back her rocket from Poppo. This upsets Kai and he decides to beat the group to become the main character again. After Poppo and Kai were defeated, Marc retrieves her rocket back with the group pitying Kai. In town, the group runs into , Islay, and , all three are working for the Guild and are also searching for Star Breaker. After finding out that both groups are looking for Star Breaker, both groups battle each other to stop the other group from finding Star Breaker first. After the Protagonist's group wins, Sherry convinces Islay and Nath to rest while the Protagonist's group search for Star Breaker, in the meanwhile, Sherry also decides to throw a welcoming party for Nath with Islay. In the outskirts of the town, the group finds , which QP initially mistaken for Shifu. NoName wants the group to flash their thighs at him one at a time, to which Marc recommends to just run away, however NoName blocks their exit with a robotic minion of his. Sora and Marc suggests to capture NoName so other people will not fall victim to him. After defeating NoName, he comments that the pain feels good. Just as Marc was about to get the authorities, NoName runs away. Later, the entire ground shakes and the group notices a in the sky. Reika explains that the castle is using Star Breaker's powers to float, which means Star Breaker is with the Guild. Reika wants to get to Star Breaker so that she can suppress her powers. Sweet Breaker appears and further explains that Reika and Star Breaker are two separate people from two separate universes and both ended up in one body due to the Mix Phenomenon; the ability to mix worlds is Reika's not Star Breaker's. Reika says that all she needs to do is fuse with Star Breaker again to suppress the mixing ability, and speculates that since Sweet Breaker can separate them, it would make sense if she can also put them back together again, and Sweet Breaker confirms this. The group fights and defeats the Flying Castle and finds Star Breaker. Star Breaker states that she wants to destroy the world because it is her dream and this is when Guildmaster appears. Guildmaster says that he teamed up with Star Breaker because he can use her to achieve his own dreams. Marc argues that Star Breaker is trying to destroy the world but Guildmaster responds by saying that he can eventually convince Star Breaker to give up on her dream, citing that Star Breaker is still young and has time to change her mind and he himself does not have that much time. Star Breaker finds Guildmaster's words absurd but amusing. The group refuses to allow Guildmaster to have his way, so Guildmaster decides to battle the group with Star Breaker. After the battle, Guildmaster contemplates his dream, concluding that the path to his dream is long but not cut off. Reika tells Star Breaker to give up and Sweet Breaker prepares to fuse them again. Star Breaker decides to just self-destruct and take the world with her, but then Sora uses her Shield Counter, QP uses her Hyper Mode, and Marc uses her 16x Big Rocket to stop Star Breaker from exploding. Sweet Breaker then fuses Reika and Star Breaker and it worked but Reika is unable to fully control her power, Star Breaker unleashed all the Mix Phenomenon powers at the last moment and Reika does not have enough energy to subdue it at the moment. The worlds mix further and further as the group is powerless to do anything but watch. Sweet Breaker led everyone to one place so that they would not get separated. Guildmaster admits that his actions led to this and accepts full responsibility and is willing to cooperate with the group however he can. Reika tries to use what energy she has left to prevent the worlds from mixing further. Sweet Breaker then temporarily increases the capacity of the world so the mixing worlds wont be annihilated immediately, so it buys the group some time to find a god that can do something about Reika's power being unleashed. Sweet Breaker states that this god would have to be more powerful than herself to stop the Mix Phenomenon. Sweet Breaker grants the group powers to cross the worlds without being separated from each other to search for a god that can help. The group, with Guildmaster tagging along, began searching for another god in the mixed world.
Back in Yukito's Base, Yukito has completed the character mixer where Protagonist can mix her cards together to attain stronger cards, such as mixing QP and dangerous pudding to get
. Back in the back alley of the town, the group finds someone on fire, Kae is on fire and laughing. Krilalaris believes Kae is protected by demon gods which the group wishes to battle Kae and Krilalaris to see if they have the god they are looking for. Kae, extinguished, and Krilalaris are defeated, they did not have any godly power at all. Back in the docks of Yukito's facility, the group finds the Waruda sister, Tomato and Mimyuu, who is with their new leader, . Nanako states that she does not want to be their new leader. Tomato exclaims that with Nanako's power, Waruda can surpass the power of god and Nanako did not like receiving this praise. The group fights the new Waruda to see if they can surpass god but it turns out they did not after defeating them. On the road that leads to QP's school, the group finds Lone Rider driving at very fast speeds; Lone Rider stops his vehicle since the group is blocking the road. Lone Rider says that he wants to see what is beyond the speed of gods by driving really fast. The group battles Lone Rider to see if he does have the speed of gods, but it again turns out that this person has no godly power. The group finds Tequila and Mescal again in some bushes and they have apparently mixed with some pigs. Tequila and Mescal are unaware of their faces resembling a pig's face, so when Marc pointed this out, they took Marc's words as an insult and attacked the group, but they were defeated. The group is worried that they would not be able to find a god in time, but then appears and asks what the group is talking about. Guildmaster says he can feel the divine power within Tomomo. QP asks Tomomo if she can follow them back to Sweet Breaker and Sora and Marc explains that the world will end soon and they need her power to stop it. Tomomo then says that the world ending is perfect, she hates this world and wants to curse it. Nothing good happened ever since Tomomo became a magical girl and her lifespan was also shortened, so she does not care i the world ends. Tomomo asks if she can destroy the world first since it is going to end anyways. QP makes a deal with Tomomo, saying that if they beat her, then Tomomo will have to help the group save the world. After beating Tomomo, Tomomo agrees to follow the group back to Sweet Breaker to help save the world. Back with Sweet Breaker, Tomomo introduces herself as Sweet Eater, one of the six gods of sweets. QP asks Tomomo why she wanted to end the world even though she is a god and Tomomo answers by saying that she was lying and just did not want to lend her help so easily. Tomomo attempts to calm Reika's powers but is unable to because she used too much power in her previous battle. Tomomo explains that they need one more person with god level powers to help. Sweet Breaker speculates that QP, Sora, and Marc might have god level powers together since they have beaten Tomomo, however the three do not know how to focus their powers as one. Guildmaster suggests wishing upon the stars for a miracle to happen and the miracle was answered with showing up. Aru has Santa powers that can make miracles happen on holy nights, and she uses this power to focus QP's, Marc's, Sora's, and her own power into one. This works, and Reika can feel her power being suppressed.
The Mix Phenomenon's progress was halted and all that is left to do is for Sweet Breaker to detach the worlds from each other. The mastermind behind the Mix Phenomenon suddenly spoke, saying how the group almost ruined everything. The mastermind is revealed to be Navi, she was invisible to everyone except Protagonist since the start of the story up until now. Navi introduces the main antagonist of the adventure, who turns out to be Protagonist. The group is shocked that Protagonist is the true mastermind and Sora asks why she is not saying anything; Protagonist had not said a single word in the entire adventure. Sweet Breaker warns the group that she can feel that Protagonist has powers greater than the gods. Protagonists still does not say anything, and Navi asks her to just follow along with for now. Navi says the she and Protagonists will not let the group separate the worlds and they must defeat Protagonist if they must separate the worlds. Navi turns Reika, Sweet Eater, Guildmaster, and Tomomo into cards, since they are final bosses and she does not want them to help the group so easily. Navi takes the cards and shuffles them into Mixdus. The group retreats to prepare to battle Protagonist. The group laments on how Protagonist is the mastermind and then Aru shows up again to cheer the group up. The group is surprised that Aru was not turned into a card like the others and then Navi suddenly appears, saying how Aru is not a final boss and she just sealed away her Santa powers. Navi tells the group that she has placed dolls across the worlds so the group can train. Marc asks why Navi is doing this and Navi answers saying that her winning is not any fun without the group giving some effort fighting back.
Eventually, the group goes to an area between all the worlds, where they find Navi and Protagonist. The group does not want to fight Protagonist because she is a friend. Navi reveals Protagonist's true name,
. Suguri thinks all this is just too silly and Navi asks Suguri to keep going along with everything and to act more like a final boss. QP asks Suguri why she is doing this, and Suguri could not respond since she still have not improved her social skills after losing them by not communicating with anyone for some time. Suguri asks the group to defeat her since it appears that nothing will progress until she is defeated. The group barely defeat Suguri in the battle but they still have not won, Suguri still has a lot of energy and the group is exhausted. Navi laughs at the group and brags about Suguri's power. Suguri then reveals Navi's true name, Sumika. Sumika made this whole game for Suguri to enjoy but Sumika is really the only one enjoying herself. Suguri says that the exercise is refreshing but all this does not feel right, she does not want to fight the group. Suguri apologizes to the group and heals their injuries; Sumika is surprised that Suguri can manipulate her program. QP thanks Suguri, Marc apologizes to Suguri for doubting her, and Sora says that it is clear who is the evil one is. So in response, Sumika laughs and declares herself as the true final boss, saying how Suguri is nothing but a puppet of hers. QP, Marc, and Sora beat Sumika, causing her to faint. Suguri congratulates the group for saving the world, and then the previous characters that were turned into cards by Sumika are now free. Sweet Breaker lets the group say their goodbyes before separating the worlds but Suguri says that everyone can meet each other again without any trouble in the future. Sweet Breaker prepares to separate the worlds but Suguri asks if she can do it instead, which Sweet Breaker allows. Suguri starts the separation and appears and lends a hand to Suguri. The worlds separate as QP, Marc, and Sora say their farewells to each other. After the separation, Sumika congratulates Suguri on her good work which Suguri responds with a sour look to Sumika. Suguri does not like playing with Sumika's shenanigans and Sumika argues that Suguri gets to meet a lot of old faces, even though its just a program. Suguri prefers just talking but Sumika sees this as boring since there is no thrill. Sumika says that something is about to happen that might be too thrilling for Suguri to handle and Suguri asks what this something is. Sumika warns Suguri that telling her what this something is might cause Suguri to die from shock. Suguri jokes that if it is possible for her to die, then she would be glad to hear Sumika on what this thing is. Sumika whispers to Suguri on what the thing is and Suguri was so shocked that she thought her heart would stop. Sumika suspects that they will arrive at the thing in about a month, which really excites Suguri. Sumika explains that this whole game was to help Suguri improve her social skills in preparation for this thing that is going to happen, Sumika couldn't see Suguri fitting into a new environment. Sumika tells Suguri to look forward to the upcoming thing, as she boosts the speed.